similar to: hidden markov models

Hi All, Does someone have an idea of how to cleverly convert a categorical timeseries into a transition matrix? Ie, I have something like: x<- c(1,1,2,1,1,2,2,2,1,2), And I want a matrix with counts and/or probabilities: > tr <- matrix(c(2,3,2,2),2,2) > tr [,1] [,2] [1,] 2 2 [2,] 3 2 Meaning that there are two transitions from 1 to 1, two from 1 to 2, three from 2 to 1

I recently upgraded from R 1.8 to 1.9. I removed 1.8 following the instructions. Html help has not worked since. When htmlhelp="TRUE" the help.start() command results in the "patience" message and nothing else happens. I am using mac osx 10.3.4. Help worked fine when I was using R 1.8. I need help help ;-] Thanks! -- Emilio A. Laca One Shields Avenue, 2306 PES Building

I need to install some geostatistics packages that are not in the binaries, for example gstat. I downloaded rm171 and installed, and I even added precomplied packages successfully. Unfortunately, I do not know how to add packages available as gstat. If you can spare a minute, could you give me a lead on this? Any other pointers on using R in mac os x will be greatly appreciated. Thank you so much

-- R Help List -- I am looking for a bivariate normal cdf routine in R. I have some fortran routines for this, which appear to be based on 15-point quadrature. Any guidance/suggestions on making these in loadable R-functions would be appreciated. Thanks, Dan =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Daniel A. Powers, Ph.D. Department of Sociology University of Texas at Austin

Dear all, does anyone have r code to perform model-averaging of regression parameters by Akaike weights, and/or to do all-possible-subsets lm modelling that reports parameter estimates, AICc and number of parameters for each model? I have been looking for these in the archive but found none. (I am aware that many of you would warn me against these methods advocated by Burnham and Anderson

Hi. I'm trying to plot the ratio of used versus unused bird houses (coded 1 or 0) versus a continuous environmental gradient (proportion of urban cover [purban2]) that I would like to convert into bins (0 - 0.25, 0.26 - 0.5, 0.51 - 0.75, 0.76 - 1.0) and I'm not having much luck figuring this out. I ran a logistic regression and purban2 ends up driving the probability of a box being

Hi AlL, I ahve this problem that my objective function is discontinous in the paramaters and I need to use methods such as nelder-mead to get around this. My question is: How do i compute standard errors to a problem that does not have a gradient? Any literature on this is greatly appreciated. Jean,

Kia ora I'm a using lme (from nlme package) with data similar to the Orthodont dataset and am getting positive log-likelihoods (>100). This seems usual and I wondered if someone could offer a possible explanation. I can supply a sample dataset if requested, but I feel almost certain that this question has been asked and answered recently. However, I can find no trace of it in the mail

Hi, When running R CMD check I'm getting a number of errors that I don't quite follow and don't know where to start looking for an answer, any hints appreciated. R CMD check trunk * checking for working latex ... OK * using log directory '/Users/ivisser/Documents/projects/ depmixProject/depmixNew/rforge/depmix/trunk.Rcheck' * using R version 2.6.2 (2008-02-08) * checking

I am trying to generate kmean of 10 clusters for a 165 x 165 matrix. i do not see any errors known to me. But I get this error on running the script Error: empty cluster: try a better set of initial centers the commands are M <-matrix(scan("R_mutual",n = 165 * 165),165,165,byrow = T) cl <- kmeans(M,centers=10,20) len = dim(M)[1] .... .... I ran the same script last night and

I would like to request help with the installation of dse in raqua in mac os x 10.3. I get the following error message after the messages indicating that parts were successfully installed. I would be most grateful for a solution. ----------------------------------------- * Installing *source* package 'setRNG' ... ** R ** inst ** help >>> Building/Updating help pages for

Dear R-helpers, I'm trying to transfer a loop from R code to C to improve performance using the .Call interface. However, I ran into problems before even getting started, and I hope (fear) I'm missing something completely obvious here. I use the following C function (passing an integer to the C function and printing it): #include <R.h> #include <Rinternals.h> SEXP

Dear All, When installing the Ruuid package (from Bioconductor) from sources on my MAC (OS X 10.3.5, R version 2.0.0) I get the following errors: m00245:~ ivisser$ R CMD INSTALL -l /Users/ivisser/Library/R/library/ /Users/ivisser/Desktop/Ruuid * Installing *source* package 'Ruuid' ... loading cache ./config.cache checking for glib-config... no checking how to run the C preprocessor...

Dear helpers, Does anyone know about a package or a function that allows to estimate Multivariate Markov-Switching Models, like MS-VAR as introduced by Krolzig(1997) with R ? Thanks a lot!! Carlo

Dear R-helpers, I made the package depmix for fitting hidden markov models. After updating R to version 2.2.0 on my PC I got the following error when installing the package from a local directory. One of the C files includes the R.h file which apparently causes problems. I call R CMD INSTALL --docs="normal" depmix and I get the following error: make[3]: *** No rule to make target

Is there a package in R that handles general linear (in-)equality + box constrained optimization? If it is not there, could anyone advise me which way to go? And/or point me to packages that solve these problems partially? best, ingmar -- Ingmar Visser Department of Psychology, University of Amsterdam Roetersstraat 15, 1018 WB Amsterdam The Netherlands http://users.fmg.uva.nl/ivisser/ tel:

Hi all, I'm writing a vignette for my package, and I would like to include some of the package help files in there as well. Is there an easy way of doing so? I tried using R CMD Rdconv to generate latex files from .Rd files but I am not sure how to include these into a .Rnw file (ie the vignette source). The resulting file from Rdconv do not readily compile using latex ... The other option I

I had written a vignette and included a \usepackage{Rd} command to make it possible to include latex'ed Rd files in the vignette. However, when loading Rd.sty texShop produces the following error: l. 180 ...d}[1]{\ifmmode\bm{#1}\else\textbf{#1}\fi} This is on Max OS X 3.9 and R 2.0.1 Has anyone seen this before and/or is it problematic? I'm not sure whether the output suffers from this

We are trying to build a human respiration model. Preliminary analysis of some breathing signals has shown that humans breathe through switching among a finite number of patterns. Hidden Markov seems to be the right approach. Since most of our code is written in R scripting language, finding an R package implementing an HMM that we can use for our prototype would be very helpful. I have been

Hi All, I was updating my help pages for a package when all of a sudden I got the following error when using R CMD INSTALL: >>> Building/Updating help pages for package 'depmix' Formats: text html latex example Error in load(zfile, envir = envir) : error reading from connection Removing all the help files makes the error disappear, but only removing the help file that I